2vkc: Difference between revisions

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-{{Seed}}
-[[Image:2vkc.png|left|200px]]
-<!--
+==Solution structure of the B3BP Smr domain==
-The line below this paragraph, containing "STRUCTURE_2vkc", creates the "Structure Box" on the page.
+<StructureSection load='2vkc' size='340' side='right'caption='[[2vkc]], [[NMR_Ensembles_of_Models | 28 NMR models]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2vkc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d9i|2d9i]]</div></td></tr>
--->
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vkc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vkc OCA], [https://pdbe.org/2vkc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vkc RCSB], [https://www.ebi.ac.uk/pdbsum/2vkc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vkc ProSAT]</span></td></tr>
-{{STRUCTURE_2vkc|  PDB=2vkc  |  SCENE=  }}
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/N4BP2_HUMAN N4BP2_HUMAN]] Has 5'-polynucleotide kinase and nicking endonuclease activity. May play a role in DNA repair or recombination.<ref>PMID:12730195</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vkc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vkc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain. This domain, which is present in both prokaryotes and eukaryotes, has previously been reported to bind to DNA and to possess nicking endonuclease activity. We determine here the solution structure of the functionally active Smr domain of the Bcl3-binding protein (also known as Nedd4-binding protein 2), a protein with unknown function that lacks other domains present in MutS proteins. The Smr domain adopts a two-layer alpha-beta sandwich fold, which has a structural similarity to the C-terminal domain of IF3, the R3H domain, and the N-terminal domain of DNase I. The most conserved residues are located in three loops that form a contiguous, exposed, and positively charged surface with distinct sequence identity for prokaryotic and eukaryotic Smr domains. NMR titration experiments and DNA binding studies using Bcl3-binding protein-Smr domain mutants suggested that these most conserved loop regions participate in DNA binding to single-stranded/double-stranded DNA junctions. Based on the observed DNA-binding-induced multimerization, the structural similarity with both subdomains of DNase I, and the experimentally identified DNA-binding surface, we propose a model for DNA recognition by the Smr domain.
-===SOLUTION STRUCTURE OF THE B3BP SMR DOMAIN===
+Solution Structure and Characterization of the DNA-Binding Activity of the B3BP-Smr Domain.,Diercks T, Ab E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE J Mol Biol. 2008 Sep 12. PMID:18804481<ref>PMID:18804481</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_18804481}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2vkc" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 18804481 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18804481}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Human]]
-VKC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKC OCA].
+[[Category: Large Structures]]
+[[Category: Ab, E]]
-==Reference==
+[[Category: Besseling, R]]
-Solution Structure and Characterization of the DNA-Binding Activity of the B3BP-Smr Domain., Diercks T, Ab E, Daniels MA, de Jong RN, Besseling R, Kaptein R, Folkers GE, J Mol Biol. 2008 Sep 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18804481 18804481]
+[[Category: Daniels, M A]]
-[[Category: Homo sapiens]]
+[[Category: Diercks, T]]
-[[Category: Single protein]]
+[[Category: Folkers, G E]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Kaptein, R]]
+[[Category: DeJong, R N]]
 [[Category: Alternative splicing]]
 [[Category: Atp-binding]]
@@ Line 41: / Line 55: @@
 [[Category: Smr]]
 [[Category: Ubl conjugation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 25 20:57:05 2009''